Hello sir. I am writing a post and describing what my issues is. I have downloaded the datasets or you can say for an example "GSE66698" dataset as in CEL.gz file, so now i wanted to ask that how should i unzip this file so that it can be readed in R GUI and also what are steps to normalize the CEL file data? Also, tell me how to download R scripts for the current CEL file?

With regards, Manorama

You don't need to unzip anything - both affy (or better yet) oligo can read in a gzipped file. As Lori mentioned, you can use ReadAffy in the affy package, but affy has a limited number of file types that it supports, and has been supplanted in most ways by the oligo package which can analyze pretty much all Affymetrix arrays, and is IMO the package you should use.

There is a vignette that you can read, that shows how to do things. If, after reading the vignette, you still have questions, please let us know.